In the present study baculovirus expressed non-structural-protein (NSP) 3A of FMD virus (FMDV) was used to develop an indirect ELISA for differentiation of FMDV infected and vaccinated animals (DIVA). Using this test, field sera (from Haryana, India) were tested where a significant reduction (P<0.05) in the carrier animals (anti-NSP antibody positive) was observed 2 years after launching FMD control programme in the state. Interestingly, population of carrier cattle was found significantly (P<0.01) higher than buffaloes. Additionally, homologous and heterologous vaccine challenge experiments (HoCEs, HtCEs) were performed with FMDV AIraq22 and AIran96. In HoCEs, animals were completely protected (PD50>32). In 1st HtCE (AIraq22 vaccine/AIran96 challege virus), the vaccine offered good protection (PD50>6) but the vice versa of vaccine and challenge virus in 2nd HtCE could not offer protection (PD50<2). High potency vaccine was found to reduce the carrier state in HoCE but in HtCEs, inspite of giving good protection in certain cases, it could not prevent the development of carrier state.